The Molecular Cytogenetics Section of the Laboratory of Genomic Diversity is engaged in comparative chromosome mapping using fluorescence in situ hybridization (FISH). With the introduction of FISH for chromosome specific DNA probes, charting the genome and mapping syntenic homology have become increasingly more rapid and economical. Fluorescence activated flow sorting (FACS) and polymerase chain reaction (PCR) amplification techniques are used to make chromosome probe sets for a wide variety of non-human species. These paint sets make reciprocal chromosome or even multidirectional painting between species possible. It has become generally appreciated that FISH greatly improves the utility of cytogenetic data for taxonomy and evolutionary studies. Chromosome painting can clarify exactly what inter-chromosomal rearrangements have occurred in evolution and the origin of humans. Homologies with the human genome of even very distantly related species are established by the use of index species and painting in a stepping stone fashion between and within mammalian orders. The principles of parsimony and outgroup comparisons are used to distinguish between conserved and derived segments of the genome and to identify the landmarks of mammalian genome evolution with a high degree of confidence. Molecular cytogenetics can also be used with confidence to transfer gene mapping data between species and to predict the chromosome location of genes thus aiding both disease and genetic trait analyses. FISH promises to simplify the use of animal models and will allow the identification of chromosome rearrangements involved in tumorigenesis and progression. For instance, the origin and progression of various human tumors can be best studied in animal models which includes the mouse, rat, hamster, but also cat and dog and other mammals. Further, reciprocal painting combined with gene mapping data will allow the construction of large-scale comparative chromosome maps between placental mammals and perhaps other animals. - Primates, Evolution, Chromosome, Animal models,